def test_extended_read_no_binning_extended_boundaries(self): #0123456789012345[67]8901234567890123456789 #.....aaaaaAAAAAA[AA]AA.................... #...............b[bb]bbBBBBBBBBBB.......... #.....CCCCCCCCCCc[cc]cc.....DDDDDDDDDDddddd peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 16, 18, resolution=1, extend_to=15) correct = np.array([3,3]) assert_array_equal(correct, peak_data) #012345678901234567890123456789012345678[9012] #.....aaaaaAAAAAAAAAA...................[....] #...............bbbbbBBBBBBBBBB.........[....] #.....CCCCCCCCCCccccc.....DDDDDDDDDDdddd[d...] peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 39, 43, resolution=1, extend_to=15) correct = np.array([1,0,0,0]) assert_array_equal(correct, peak_data) #01234567890123456789012345678901234567890[123] #.....aaaaaAAAAAAAAAA.....................[...] #...............bbbbbBBBBBBBBBB...........[...] #.....CCCCCCCCCCccccc.....DDDDDDDDDDddddd[....] peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 41, 44, resolution=1, extend_to=15) correct = np.array([0,0,0]) assert_array_equal(correct, peak_data)
def test_extended_reads_extended_boundaries_binning(self): #012345678901234567[8901234|5678901|2345678]90123 #.....aaaaaAAAAAAAA[AA.....|.......|.......]..... #...............bbb[bbBBBBB|BBBBB..|.......]..... #.....CCCCCCCCCCccc[cc.....|DDDDDDD|DDDdddd]d.... peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 18, 39, resolution=7, extend_to=15) correct = np.array([3,2,1]) assert_array_equal(correct, peak_data)
def test_extended_read_no_binning_extended_boundaries_edge_case(self): #[012345]67890123456789012345678901234567890123 #[.....a]aaaaAAAAAAAAAA........................ #[......].........bbbbbBBBBBBBBBB.............. #[.....C]CCCCCCCCCccccc.....DDDDDDDDDDddddd.... peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 0, 6, resolution=1, extend_to=15) correct = np.array([0,0,0,0,0,2]) assert_array_equal(correct, peak_data) #[01234]567890123456789012345678901234567890123 #[.....]aaaaaAAAAAAAAAA........................ #[.....]..........bbbbbBBBBBBBBBB.............. #[.....]CCCCCCCCCCccccc.....DDDDDDDDDDddddd.... peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 0, 5, resolution=1, extend_to=15) correct = np.array([0,0,0,0,0]) assert_array_equal(correct, peak_data)
def test_extended_read_binning(self): peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 3, 43, resolution=5, extend_to=15) #012[34567|89012|34567|89012|34567|89012|34567|89012] #...[..aaa|aaAAA|AAAAA|AA...|.....|.....|.....|.....] #...[.....|.....|..bbb|bbBBB|BBBBB|BB...|.....|.....] #...[..CCC|CCCCC|CCccc|cc...|..DDD|DDDDD|DDddd|dd...] correct = np.array([2,2,3,3,2,2,1,1]) assert_array_equal(correct, peak_data)
def test_extended_read_no_binning(self): peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 3, 40, resolution=1, extend_to=15) #012|3456789012345678901234567890123456789| #...|..aaaaaAAAAAAAAAA....................| #...|............bbbbbBBBBBBBBBB..........| #...|..CCCCCCCCCCccccc.....DDDDDDDDDDddddd| correct = np.array([0,0,2,2,2,2,2,2,2,2,2,2,3,3,3,3,3,1,1,1,1,1,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1]) assert_array_equal(correct, peak_data)
def test_non_extended_read_binning(self): peak_data = bam_parser._read_samfile_region(self.samfile, 'chr1', 3, 43, resolution=5, extend_to=None) correct = np.array([1,2,2,2,2,2,1,0]) assert_array_equal(correct, peak_data)